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Looking at the script again, I think I see where the problem is coming in. There is an un-needed "If false :jump" command at the start of the script without anything that would set it as true or false. As such, whether it jumps to the "no room for items" or not is determined by whatever value is already in that ram address from any other event. (This ram address is one that gets used by most scripts as a temporary place to store values such as whether you answered yes or no, or whether there is room for an item or not, etc.)

Enter the gameshark code 010173D1 and try talking to the Pokeball again, then just turn the code off. Don't keep it on the whole time you are talking to the Pokeball either. Have the code on, talk to the Pokeball, then turn the code off while it is showing the text. There is another check in the script after the text comes up, so you won't want it to continue forcing that value to be x01. You just want it to do that long enough to make the event run.

Basically, this will just force it to be "true" while the code is on. You'll want to turn the code off when you're done though, because continuing to play with this code on would make the game assume you answered "yes" to every question regardless of what you actually pressed and could cause other weird things, so don't keep it on all the time. But it aught to fix it so you can pickup the badges.

EDIT: Or, if you wanted to "hack the hack" to just fix the actual error, you could just open the rom in Johtomap, load that map for the train station, click on the Pokeball, and change its script pointer to 44FD instead of 44FA and it won't even load that pointless check and will just run the code like it is supposed to.

Looking at the script again, I think I see where the problem is coming in. There is an un-needed "If false :jump" command at the start of the script without anything that would set it as true or false. As such, whether it jumps to the "no room for items" or not is determined by whatever value is already in that ram address from any other event. (This ram address is one that gets used by most scripts as a temporary place to store values such as whether you answered yes or no, or whether there is room for an item or not, etc.)

Enter the gameshark code 010173D1 and try talking to the Pokeball again, then just turn the code off. Don't keep it on the whole time you are talking to the Pokeball either. Have the code on, talk to the Pokeball, then turn the code off while it is showing the text. There is another check in the script after the text comes up, so you won't want it to continue forcing that value to be x01. You just want it to do that long enough to make the event run.

Basically, this will just force it to be "true" while the code is on. You'll want to turn the code off when you're done though, because continuing to play with this code on would make the game assume you answered "yes" to every question regardless of what you actually pressed and could cause other weird things, so don't keep it on all the time. But it aught to fix it so you can pickup the badges.

It fixes some major bugs, so if you haven't finished the game yet or haven't played it. This is the version to get.

-Fixed some more spelling and grammar issues.
-Fixed bug which allowed you to fight FLYNN multiple times.
-Fixed a bug which made a crucial item ball unobtainable for some people.
-Fixed being able to view town map on house walls where there was no map.

From the looks of it, this is going to be my favourite Pokémon romhack.

I especially like that artwork of the protagonists and the starters you put on the website.

Spoiler:

Are we meant to be able to see a couple of the original locations from Gold/Silver on that bottom-left island on the Town Map when scrolling through, though?
Another issue I've noticed with the Town Map, this time in Kanto: the cursor gets stuck in an infinite loop when you get near the Pokémon League area.

From the looks of it, this is going to be my favourite Pokémon romhack.

Are we meant to be able to see a couple of the original locations from Gold/Silver on that bottom-left island on the Town Map when scrolling through, though?
Another issue I've noticed with the Town Map, this time in Kanto: the cursor gets stuck in an infinite loop when you get near the Pokémon League area.

I've listed that in the readme.
The infinite loop thing I think is left over from Gold considering you're not able to get to the rest of Kanto until after the elite four.

Anyway, we've come across a game breaking bug, but I have a way to fix it.
To avoid it, whatever you do, do not save your game inside Acre Forest. It will make you unable to move and progress any further. If you happen to get this bug, this is how you fix it:

1. Rename your save and load it in Pokemon Gold
2. Use DIG or an ESCAPE ROPE to exit the current area
3. Save inside the nearest Pokemon Center
4. Rename and load your save back into Pokemon Bronze

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